Abstract Background Autoimmune pancreatitis (AIP) is often misdiagnosed as pancreatic cancer (PC). Both conditions accumulate 18F-fluorodeoxyglucose (FDG), so FDG positron emission tomography (FDG-PET) is not discriminatory. This study aimed to evaluate the pattern of FDG accumulation, and the change in FDG uptake after steroid treatment in AIP and PC. Methods We compared FDG-PET patterns between 18 patients with AIP and 20 patients with PC, and also evaluated the short-term changes in FDG uptake after steroid therapy. Results FDG uptake was observed in 88.9% in AIP and 90.0% in PC. FDG uptake in extra-abdominal lymph nodes was seen more frequently in AIP, and uptake in salivary glands, eyes and biliary ducts was seen only in AIP. Follow- up PET was performed in 6 AIP patients and in 3 PC patients. Changes in SUVmax after steroid therapy were estimated within 1 week in 5 AIP patients and in all 3 PC patients, retrospectively. In 4 AIP patients, the change in SUVmax was more than 10%. On the other hand, in PC, SUVmax increased or remained almost unchanged (within 10%). Conclusions FDG-PET pattern at baseline, and a decrease in FDG uptake after a short steroid trial can be